Control of information

by John Sulston

MODERN sequencers run 96 DNA samples at a time and can do eight runs per day. Some of the bigger labs may have 100 or more machines in operation at once. These machines initially accepted only 24 samples, with each run lasting at least 14 hours. As the sole manufacturer, Applied Biosystems Inc (ABI) sought to retain control of the data analysis by making its customers use its own proprietary software.

Even though the sequencers were effective, we clearly needed to control the software. To finish the sequence properly, we also needed easy access to the raw data to evaluate their quality from point to point. The software’s display system was inconvenient and slowed us down. We refused to be dependent on a commercial company for handling and processing the data we were producing. (ABI even
sought to control the analysis of the sequence itself.)

I was completely obsessed with getting the sequence data out quickly. The best way to drive the science was to get the sequencing machines running faster and cheaper, and to get the maximum data out so that theorists worldwide could interpret them.

One summer Sunday afternoon, I was sitting on the lawn at home with printouts strewn around me as I tried to decrypt the ABI file that stored our trace data. The file was not deliberately encrypted: it was set up like a Christmas tree and I had to track from one point to another. Within a few days my colleagues and I had written display software enabling us to show our trace data. We then decrypted more of the ABI files, giving us complete freedom to design our own display and analysis systems. This transformed our productivity.

ABI was none too happy with what we had done. We had been negotiating with the company to purchase a key to unlock the files, but it was clear that ABI would still control file access. There was the real risk that ABI might re-encrypt its files to prevent us from gaining access. But ABI eventually realised that its only option was to make its file formats public. We soon became one of ABI’s biggest customers.

This was my first experience battling for control of information. It was also a foretaste of the much larger battles that would characterise the human genome project.